A specific graphene field-effect transistor (GFET)-based aptasensor was developed for the detection of highly toxic Ochratoxin A (OTA), which relies on an array of GFETs integrated on a single silicon chip. We experimentally studied the aptamer reconfiguration process during binding a specific target molecule, i.e. OTA, the interaction of an aptamer with graphene, and how the variation of ionic strength of a solution influences the sensitivity of our biosensor. We suggest that aptamer, when free-standing, is weakly adsorbed on graphene’s surface via π-π stacking, which is experimentally confirmed by a left-shift of charge neutrality point in transfer characteristic of GFET (n-doping) compared to PBASE-modified graphene. On the other hand, when the aptamer binds the OTA molecule, it undergoes 3D reconfiguration into G-quadruplex and desorbs from the graphene surface, which initiates the right-shift of charge neutrality point (p-doping). Finally, we showed that, by decreasing ionic strength 10 times, the sensitivity can be improved due to increased electrostatic gating from aptamer G-quadruplex structure, which confirms the idea of aptamer desorption from the graphene surface upon OTA binding.